March 26, 2014

Nowadays, regions with relatively lower CpG density are gaining importance in DNA methylation studies. This is based on the fact that a majority of CpG rich regions (CpG islands) are non-dynamic and less variant in terms of methylation status probed across a variety of tissues and cell populations (Irizarry 2009, Ziller 2013). It is now proven that methylation is more dynamic along the CpG shores (< 2kb flanking CpG Islands) and CpG shelves (<2kb flanking outwards from a CpG shore). While it is easy to retreive the genomic co-ordinates of CpG Islands from UCSC browser, public resources for retrieving the genomic co-ordinates for shores and shelfs were missing or scarce. Here, I am displaying the code (in R using Bioconductor package GenomicRanges) I use for generating objects for CpG islands, CpG island shores and CpG island shelves. The resulting objects are GRanges objects which could be used in multiple downstream applications in Bioconductor related packages.